+Open data
-Basic information
Entry | Database: PDB / ID: 2h64 | ||||||
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Title | Crystal structure of a ternary ligand-receptor complex of BMP-2 | ||||||
Components |
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Keywords | Hormone/Growth Factor / TGF-beta superfamily / ligand-receptor complex / Hormone-Growth Factor COMPLEX | ||||||
Function / homology | Function and homology information Signaling by Activin / neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / activin receptor activity, type II / positive regulation of transforming growth factor beta2 production / inhibin binding / Mullerian duct regression / Signaling by BMP ...Signaling by Activin / neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / activin receptor activity, type II / positive regulation of transforming growth factor beta2 production / inhibin binding / Mullerian duct regression / Signaling by BMP / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / heart formation / atrioventricular node cell development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / lymphatic endothelial cell differentiation / mesendoderm development / negative regulation of steroid biosynthetic process / ameloblast differentiation / tricuspid valve morphogenesis / positive regulation of activin receptor signaling pathway / positive regulation of extracellular matrix constituent secretion / atrioventricular valve development / activin receptor activity / dorsal aorta morphogenesis / negative regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / central nervous system neuron differentiation / lung vasculature development / lymphangiogenesis / cardiac right ventricle morphogenesis / negative regulation of insulin-like growth factor receptor signaling pathway / mesenchyme development / thyroid-stimulating hormone-secreting cell differentiation / venous blood vessel development / pharyngeal arch artery morphogenesis / aortic valve development / BMP binding / telencephalon regionalization / hindlimb morphogenesis / positive regulation of phosphatase activity / regulation of cardiac muscle cell proliferation / negative regulation of muscle cell differentiation / negative regulation of smooth muscle cell migration / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / lateral mesoderm development / regulation of lateral mesodermal cell fate specification / ventricular compact myocardium morphogenesis / pericardium development / retina vasculature development in camera-type eye / pituitary gland development / mitral valve morphogenesis / BMP receptor complex / dorsal/ventral axis specification / BMP receptor activity / co-receptor binding / regulation of cellular senescence / neural crest cell development / embryonic foregut morphogenesis / telencephalon development / cardiac epithelial to mesenchymal transition / ectoderm development / BMP receptor binding / positive regulation of odontoblast differentiation / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / cardiac conduction system development / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / Transcriptional regulation by RUNX2 / phosphatase activator activity / positive regulation of astrocyte differentiation / pattern specification process / artery development / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / activin binding / cardiac muscle cell differentiation / cellular response to BMP stimulus / activin receptor signaling pathway / outflow tract septum morphogenesis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / kinase activator activity / positive regulation of ossification / astrocyte differentiation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Mueller, T.D. / Sebald, W. / Weber, D. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2007 Title: A silent H-bond can be mutationally activated for high-affinity interaction of BMP-2 and activin type IIB receptor. Authors: Weber, D. / Kotzsch, A. / Nickel, J. / Harth, S. / Seher, A. / Mueller, U. / Sebald, W. / Mueller, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h64.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h64.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 2h64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h64 ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h64 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains half of the hexameric assembly. The biological unit can be obtained by applying the symmetry operation: y, x, -z+1 |
-Components
#1: Protein | Mass: 12940.861 Da / Num. of mol.: 1 / Mutation: L100K, N102D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Production host: Escherichia coli (E. coli) / References: UniProt: P12643 |
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#2: Protein | Mass: 14199.918 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMPR1A, ACVRLK3, ALK3 / Production host: Escherichia coli (E. coli) References: UniProt: P36894, receptor protein serine/threonine kinase |
#3: Protein | Mass: 11648.771 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acvr2b / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KQI1, UniProt: P27040*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.58 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.75 Details: 30% PEG3350, 0.1M Tris-HCl pH 8.75, 0.2M NH4CH3COO, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 8, 2005 / Details: Osmic VariMax HR |
Radiation | Monochromator: Osmic VariMax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→500 Å / Num. all: 42780 / Num. obs: 42606 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.069 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4140 / Rsym value: 0.514 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→500 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.92→500 Å
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Refine LS restraints |
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